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Coexpression cluster:C4628: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.70e-33!94;UBERON:0001016!4.70e-33!94;UBERON:0005743!5.35e-32!86;UBERON:0001017!1.38e-31!82;UBERON:0007023!5.62e-28!115;UBERON:0001049!2.65e-27!57;UBERON:0005068!2.65e-27!57;UBERON:0006241!2.65e-27!57;UBERON:0007135!2.65e-27!57;UBERON:0000924!2.18e-26!173;UBERON:0006601!2.18e-26!173;UBERON:0000955!2.53e-26!69;UBERON:0006238!2.53e-26!69;UBERON:0004121!9.25e-26!169;UBERON:0002616!1.11e-25!59;UBERON:0002346!4.63e-25!90;UBERON:0003075!1.26e-24!86;UBERON:0007284!1.26e-24!86;UBERON:0000033!3.54e-23!123;UBERON:0000153!4.87e-22!129;UBERON:0007811!4.87e-22!129;UBERON:0003080!5.41e-21!42;UBERON:0002780!1.36e-20!41;UBERON:0001890!1.36e-20!41;UBERON:0006240!1.36e-20!41;UBERON:0000475!4.19e-19!365;UBERON:0003056!5.52e-18!61;UBERON:0000468!3.04e-17!659;UBERON:0000481!4.33e-17!347;UBERON:0002020!6.43e-17!34;UBERON:0003528!6.43e-17!34;UBERON:0001893!1.02e-16!34;UBERON:0002791!2.93e-16!33;UBERON:0001869!1.37e-15!32;UBERON:0004111!1.16e-14!241;UBERON:0000477!2.12e-14!286;UBERON:0000922!3.49e-13!612;UBERON:0000956!1.77e-12!25;UBERON:0000203!1.77e-12!25;UBERON:0002619!2.01e-12!22;UBERON:0000467!2.55e-12!625;UBERON:0000480!3.44e-12!626;UBERON:0000483!6.03e-12!309;UBERON:0000119!7.00e-12!312;UBERON:0002050!9.43e-12!605;UBERON:0005423!9.43e-12!605;UBERON:0000062!1.11e-11!511;UBERON:0000025!1.22e-11!194;UBERON:0000923!1.93e-11!604;UBERON:0005291!1.93e-11!604;UBERON:0006598!1.93e-11!604;UBERON:0002532!1.93e-11!604;UBERON:0001950!2.96e-11!20;UBERON:0000064!2.28e-10!219;UBERON:0003076!1.76e-07!15;UBERON:0003057!1.76e-07!15
|ontology_enrichment_uberon=UBERON:0000073!4.70e-33!94;UBERON:0001016!4.70e-33!94;UBERON:0005743!5.35e-32!86;UBERON:0001017!1.38e-31!82;UBERON:0007023!5.62e-28!115;UBERON:0001049!2.65e-27!57;UBERON:0005068!2.65e-27!57;UBERON:0006241!2.65e-27!57;UBERON:0007135!2.65e-27!57;UBERON:0000924!2.18e-26!173;UBERON:0006601!2.18e-26!173;UBERON:0000955!2.53e-26!69;UBERON:0006238!2.53e-26!69;UBERON:0004121!9.25e-26!169;UBERON:0002616!1.11e-25!59;UBERON:0002346!4.63e-25!90;UBERON:0003075!1.26e-24!86;UBERON:0007284!1.26e-24!86;UBERON:0000033!3.54e-23!123;UBERON:0000153!4.87e-22!129;UBERON:0007811!4.87e-22!129;UBERON:0003080!5.41e-21!42;UBERON:0002780!1.36e-20!41;UBERON:0001890!1.36e-20!41;UBERON:0006240!1.36e-20!41;UBERON:0000475!4.19e-19!365;UBERON:0003056!5.52e-18!61;UBERON:0000468!3.04e-17!659;UBERON:0000481!4.33e-17!347;UBERON:0002020!6.43e-17!34;UBERON:0003528!6.43e-17!34;UBERON:0001893!1.02e-16!34;UBERON:0002791!2.93e-16!33;UBERON:0001869!1.37e-15!32;UBERON:0004111!1.16e-14!241;UBERON:0000477!2.12e-14!286;UBERON:0000922!3.49e-13!612;UBERON:0000956!1.77e-12!25;UBERON:0000203!1.77e-12!25;UBERON:0002619!2.01e-12!22;UBERON:0000467!2.55e-12!625;UBERON:0000480!3.44e-12!626;UBERON:0000483!6.03e-12!309;UBERON:0000119!7.00e-12!312;UBERON:0002050!9.43e-12!605;UBERON:0005423!9.43e-12!605;UBERON:0000062!1.11e-11!511;UBERON:0000025!1.22e-11!194;UBERON:0000923!1.93e-11!604;UBERON:0005291!1.93e-11!604;UBERON:0006598!1.93e-11!604;UBERON:0002532!1.93e-11!604;UBERON:0001950!2.96e-11!20;UBERON:0000064!2.28e-10!219;UBERON:0003076!1.76e-07!15;UBERON:0003057!1.76e-07!15
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}}
}}

Revision as of 14:15, 5 September 2012


Full id: C4628_gastric_lung_medulla_astrocytoma_cerebellum_spinal_pineal



Phase1 CAGE Peaks

Hg19::chr6:80247047..80247100,-p2@LCA5
Hg19::chr6:80247105..80247133,-p1@LCA5
Hg19::chr6:80247140..80247158,-p3@LCA5


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.70e-3394
nervous system4.70e-3394
central nervous system1.38e-3182
adult organism5.62e-28115
neural tube2.65e-2757
neural rod2.65e-2757
future spinal cord2.65e-2757
neural keel2.65e-2757
ectoderm2.18e-26173
presumptive ectoderm2.18e-26173
brain2.53e-2669
future brain2.53e-2669
ectoderm-derived structure9.25e-26169
regional part of brain1.11e-2559
neurectoderm4.63e-2590
neural plate1.26e-2486
presumptive neural plate1.26e-2486
head3.54e-23123
anterior region of body4.87e-22129
craniocervical region4.87e-22129
anterior neural tube5.41e-2142
regional part of forebrain1.36e-2041
forebrain1.36e-2041
future forebrain1.36e-2041
organism subdivision4.19e-19365
pre-chordal neural plate5.52e-1861
multi-cellular organism3.04e-17659
multi-tissue structure4.33e-17347
gray matter6.43e-1734
brain grey matter6.43e-1734
telencephalon1.02e-1634
regional part of telencephalon2.93e-1633
cerebral hemisphere1.37e-1532
anatomical conduit1.16e-14241
anatomical cluster2.12e-14286
embryo3.49e-13612
cerebral cortex1.77e-1225
pallium1.77e-1225
regional part of cerebral cortex2.01e-1222
anatomical system2.55e-12625
anatomical group3.44e-12626
epithelium6.03e-12309
cell layer7.00e-12312
embryonic structure9.43e-12605
developing anatomical structure9.43e-12605
organ1.11e-11511
tube1.22e-11194
germ layer1.93e-11604
embryonic tissue1.93e-11604
presumptive structure1.93e-11604
epiblast (generic)1.93e-11604
neocortex2.96e-1120
organ part2.28e-10219
posterior neural tube1.76e-0715
chordal neural plate1.76e-0715


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CHD2#1106310.34402283411690.0009033701102746880.00662642723324752
EBF1#187938.9064668465690.00141523283560980.00918902717552082
ELF1#199734.258097958807540.01295179875054610.0464772165237865
FOS#235338.99795530889440.001372499272417130.00901638265894908
HMGN3#932438.178547723350590.001827766942164210.0109154935768921
IRF1#365937.63716375356390.002244692747297240.0128696456870321
IRF3#3661346.98195221148969.63568551583244e-060.000254126605956572
NFYA#4800318.42558069983050.0001598135507814160.0020020112066763
NFYB#4801316.75979325353650.0002123649923296180.00246627237116791
RFX5#5993312.04791082719510.0005717246050312580.0048675589814021
SETDB1#9869340.32002617801051.52461559299059e-050.000360003002297862
SIN3A#2594235.408884726815140.006318961977991520.0278188285638181
SP1#666735.69838137814090.005403962701712170.0247819645474715
SP2#6668326.15353049384465.58768218891694e-050.00094230896193815
SRF#6722313.79717826216780.0003806615025800190.00376333838204796
YY1#752834.911170749853860.008441455341808260.0331098942593275
ZBTB7A#5134137.35190930787590.002516255860282270.0140878763692516
ZEB1#6935211.25895467836260.01010222676646330.0378254924627204



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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